Hello manishk,
I guess there is no folder like windows' Program Files , but it doesn't matter much. I put my .exe files and setup ones in my Home folder.
But we can make a Program Files folder of our own inside Home and store our .exe files or anything else we want, in it.

Besides, if we were wise enough to create a /home partition during installation,
our Home folder will always be there safe and untouched when we do an upgrade.

I guess I have a similar question. By convention, in Linux, where do you typically install/unpack applications? Your /home/<username> folder? Or is it better to put them in /usr/share? I have to get used to this new filesystem. I don't think I'd like my home folder to be stuffed with 100s of apps and their folders. I like to keep it pretty clean and organized. Sorry this isn't really related to Wine but just a general Linux question.